A Young Researcher's Guide to NME/Nm23/NDP Kinase
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PERIODICUM BIOLOGORUM UDC 57:61 VOL. 120, No 1, 3–9, 2018 CODEN PDBIAD DOI: 10.18054/pb.v120i1.6229 ISSN 0031-5362 review article A young researcher’s guide to NME/Nm23/NDP Kinase Abstract MAJA HERAK BOSNAR*1 1 MARTINA RADIĆ Nucleoside diphosphate kinases (NDPKs) catalyze the exchange of the HELENA ĆETKOVIĆ2 terminal phosphate from trinucleotides to dinucleotides through a high- 1 Laboratory for Protein Dynamics, energy phosphohistidine intermedier. They are encoded by NME genes and Ruđer Bošković Institute, Zagreb, Croatia have been found, with a few exceptions, in all living beings. Besides their 2 Laboratory for Molecular Genetics, well-known function as key regulators of the cellular nucleotide homeostasis, Ruđer Bošković Institute, Zagreb, Croatia they have been appointed numerous additional biochemical and biological *Correspondence: functions. The discovery of NME1/NDPK A as the first metastasis suppres- Maja Herak Bosnar sor opened new avenues in cancer research. Although the precise role of NME e-mail: [email protected] genes/proteins in cancer dissemination is not yet revealed, it seems that fur- ther intensive research in this field may lead to new advances in cancer di- agnosis and prognosis, as well as encourage new therapeutic strategies. Abbreviations: NDPK – nucleoside diphosphate kinase MIF – macrophage migration inhibitory factor MDM2 – mouse double minute 2 homolog INTRODUCTION EBNA 1 – 3C – Epstein-Barr nuclear antigen 1–3C TGF-b – transforming growth factor b ucleoside-diphosphate kinases (NME/Nm23/NDPK) constitute LPA1 – lysophosphatidic acid receptor 1 Na family of evolutionary conserved enzymes present in all three MPA – medroxyprogesterone acetate domains of life (1). The NDPK was discovered in the mid-20th century STRAP – Serine/Threonine Kinase Receptor by its biochemical activity consisting of the removal of the terminal Associated Protein phosphate from a nucleoside triphosphate (mainly ATP) and its addition MLS – mitochondrial localization signal domain to all other (d)NDPs. It is generally considered to be a housekeeping TRF1 – Telomeric Repeat Binding Factor 1 ICAP1a – integrin cytoplasmic domain-associated enzyme since it is in charge of the maintenance of the cellular NTP pool protein 1alpha (2). A huge interest for this enzyme started in early nineties when it was discovered that a gene named nm23 (non-metastatic clone 23, also known as NME), responsible for metastasis suppression in the murine melanoma model system (3) is actually encoding one of the subunits of NDPK, NDPK A. The NME/Nm23/NDPK family members have been assigned a vast range of biological functions spanning from metastasis suppression, proliferation and development to ciliary functions and ve- sicular transport (4). Despite comprehensive studies done so far in this field, there are still essential questions that have not been answered. The exact mechanism by which the members of the NME/Nm23/NDPK family execute their biological functions still remains to be unraveled. Structure, function and intracellular localization of NME/NDPK members Nucleoside diphosphate kinases (NDPKs) catalyze the exchange of g-phosphate between triphosphates and diphosphates through a high- energy phosphohistidine intermedier (5). They are encoded by the NME Received December 21, 2017. genes. Ten such genes have been found in humans (4). On the basis of Revised January 17, 2018. phylogenetic studies, the exon-intron structure and the presence/absence Accepted January 19, 2018. of specific protein domains, the vertebrate NME proteins have been separated into two groups (Figure 1) (6). Herak Bosnar et al. NME/Nm23/NDP Kinase kDa subunits A and B are 88% identical in their amino acid sequence. Both proteins are ubiquitously expressed and display mainly cytoplasmic localization but can also be found elsewhere in the cell (Figure 2) (8). A transcript encoding a longer form of NDPK A (9), as well as a re- adthrough transcript encoding a part of the NDPK A and the complete NDPK B have been reported (10). The third gene/protein in the Group I named DR-Nm23 (NME3 or NDPK C) has also been reported and seems to be at least partially localized in the mitochondria. NME3 po- ssesses a 17 amino acid N-terminal hydrophobic sequen- ce which could anchor the protein in the membrane but it is not considered to be a regular mitochondrial signaling sequence (11). The NDPK D (NME4/Nm23-H4) is, however, a true mitochondrial NDPK with a canonical sequence which targets the protein to mitochondria (12). All Group I members exhibit the NDPK activity in their hexameric form with similar kinetic parameters. They possess nine specific residues that have been essential for Figure 1. Schematic representation of NME proteins domains in the stability of the NDP kinase and its activity (13). Be- human and sponge. Proteins are represented on a scale 1:10 (1mm sides this housekeeping role in the synthesis of nucleoside = 10 amino acids). The number of amino acids is displayed on the triphosphates, the NME/NDPK proteins have been assi- right side of the schematic representation of the gene. Protein do- mains have been indicated with boxes, and each protein has been gned several additional biochemical functions. One of searched against SMART/Pfam databases. Abbreviations of do- them is the His-protein kinase which includes the transfer main names are retrieved from SMART/Pfam databases and in- of a high-energy phosphate from the phosphorylated in- dicated in the figure. Shortened name MLS stands for mitochon- termediate to another protein (14, 15). There has also been drial localization signal domain. evidence that the NME proteins may function as trans- criptional modulators (16), exonucleases (17) and have a scaffold function (18). NME1-4 Group I protein members ( ) are generally NME Group II encompasses NME5-9 and, in con- highly homologous among themselves and compared to trast to the Group I members, they are more divergent their orthologs in different species (58-88% amino acid among themselves (28-45% amino acid identity) and dis- homology). Their corresponding genes have a similar ex- similar to Group I proteins (25-34% amino acid identity). on-intron structure, as well (7). The NME1/NDPK A and They possess either a single or several NDK domains. NME2/NDPK B subunits form the main cellular nucle- Their tentative multimeric forms have not yet been eluci- oside diphosphate kinase which executes at least 80% of dated. So far, the enzymatic activity was reported only for the cellular NDPK function. The identically folded subu- the NME6 (19), although the evidence for its NDPK ac- nits can assemble into enzymatically active hexamers in tivity is questionable. Compared to the human NME1 all possible combinations (A6, A5B1,....B6) (2). The 17 and NME2, the NME6 protein has seven additional Figure 2. Subcellular localization of GFP-Nm23-H2. Human melanoma cell line WM793B transfected with pEGFPC1-nm23-H2. Fluorescent staining is visible in the cytosol and the nuclei with greater incidence in the cytoplasmic region. Scale bar represents 10 µm. 4 Period biol, Vol 120, No 1, 2018. NME/Nm23/NDP Kinase Herak Bosnar et al. residues at the N-terminus and 23 additional residues at usually associated with “higher” metazoans. The possible the C-terminus. It has one extra amino acid at the posi- function of the NMEGpI (ancestral type protein, the pre- tion Leu-30 and three additional residues in the Kpn-loop cursor of Group I proteins) is not yet established in simple which lies in the catalytic site and is essential for the main- metazoans but it is possible that it participates in ancient tenance of the hexameric structure, a prerequisite for the precursor processes, which can be viewed as a foundation NDPK activity. It is also possible that the elongated C- for the complex signaling networks in higher animals. terminus in NME6 (and NME5 as well) disrupts the Our recent work on the NME homolog from filasterean hexameric form (20). Human NME6 does not possess the Capsospora owcarzaky, a close unicellular relative of ani- canonical mitochondrial signaling sequence but potential mals (25) reveals similar features which indicate that the mitochondrial targeting sequences have been observed in NME protein did not change significantly in the transi- homologs of NME6 in non-bilaterian metazoans (21). tion to multicellularity. The Group II members usually do not possess all nine It has been shown that NME5-8 have already been residues considered to be crucial for the NDPK activity. present in the common ancestor of choanoflagellates and They differ considerably from the Group I by having -ei metazoans and emerged at the time of eukaryote radiation ther one or several NDK domains (NME7 and NME8 (23). Most Group II members are present in early-branch- have two and three NDK domains, respectively), while ing eukaryote lineages. Two exceptions are NME8, which some of the NME representatives have additional do- is probably a choanoflagellate/metazoan innovation, and mains. Almost all metazoan NME5 proteins possess a NME9, which originated from an incompletely translo- C-terminal DPY-30 domain, NME7 has a DM10 domain cated duplication of NME8 after separation of eutherians while NME8 and NME9 have thioredoxin domains (7). and metatherians. The NME10 displays a separate evolu- The Group II members differ from the Group I members tionary history since it seems that its NDK domain was especially in the length of their N and C termini (Figure inserted relatively recently (7). The evolutionary studies 1). As mentioned earlier, the NME6 was reported to be of the Group II genes/proteins underscore their necessity located in the mitochondria. Interestingly, all members in the physiology of every living cell although there has of the Group II, except NME6, encode proteins mainly been no systematic research to reveal their function. located in cilia or flagella of spermatids or spermatozoa (22). Their role in these cellular structures remains to be NME1 – a pioneer in metastasis elucidated.